## [1] "O77_p5_con_R1_2.hicup.bam"

Truncation & Mapping

Truncation Frequency

Category Read 1 Read 2
Total 67,469,988 67,469,988
Not Truncated 38,790,372 36,700,618
Truncated 28,679,616 30,769,370

Truncated Read Length

Category Read 1 Read 2
Average Length Truncated 47.2 47.1

Mapping Efficiency

Category Read 1 Read 2
Too Short To Map 5,024,738 5,126,162
Unique Alignments 57,419,111 55,772,438
Multiple Alignments 2,464,572 2,499,157
Failed To Align 2,561,567 4,072,231
Paired 47,765,077 47,765,077

Truncation and Mapping Bar Plot

Filtering

Filtering Breakdown by Category

Category Count
Valid Pairs 25,870,377
Invalid Pairs 21,894,700
Same Circularised 1,380
Same Dangling Ends 4,788,107
Same Fragment Internal 8,648,239
Re Ligation 6,094,287
Contiguous Sequence 104,180
Wrong Size 2,258,507
Total Pairs 47,765,077

Filtering Breakdown Pie Chart

Ditag Length Distribution

Frequency Line Plot

Deduplication

Deduplication Summary Table

Category All Ditags Unique Ditags
Read Pairs 25,870,377 31,333
Cis-close (<10Kbp) 2,744,526 2,943
Cis-far (>10Kbp) 17,448,078 17,104
Trans 5,677,773 11,286

Deduplication Bar Chart

Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data

Babraham Bioinformatics